Dihydrofolate reductase (DHFR) is a ubiquitous enzyme that is the target for the antifolate drugs. The antifolates are of continuing importance not only in neoplastic disease, but also of increasing utility in autoimmunine disorders, AIDS-related opportunistic complications (including parasitic and bacterial infections) and such infections in general. Problems of extensive toxicity and lack of selectivity of the currently available drugs such as methotrexate (MTX) and trimethoprim (TMP) provide the impetus for further study. The correlation techniques of QSAR (quantitative structural activity relationships) are such an approach to gain understanding of the forces that mediate the interaction of ligands (drugs) with their targets, thus suggesting the minimum number of structural variations in a base compound to achieve an inhibitor that is uniquely selective and potent. DHFR is a unique system to analyze via QSAR since not only are the X-ray crystallographic structures well defined for the reductases from chicken liver, E. coli and L. casei, but also hundreds of closely related antifolate inhibitors have been synthesized. Using methods developed in this laboratory, DHFR from several animal sources have been extensively purified and are available for investigation of enzymatic properties, mechanism of action, and interaction with metabolic inhibitors and drugs, in collaborative studies. The inhibition of chicken liver DHFR by a series of 5- (substituted benzyl)-2, 4-diaminopyrimidines was analyzed in terms of parameters relating to substituents on the aromatic side chains of the inhibitor, including hydrophobicity, molar refractivity, the Hammet constant, certain indicator variables and polar and non-polar interactions. While the QSAR results appear to be in general agreement with X-ray crystallographic models at 2.8-A resolution, prediction of specific structural details is not yet possible.